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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#ifndef APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP |
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#define APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP |
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#include "selection/SelectionEvaluator.hpp" |
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#include "selection/SelectionManager.hpp" |
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#include "applications/staticProps/StaticAnalyser.hpp" |
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#include "utils/Tuple.hpp" |
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namespace OpenMD { |
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class SCDElem { |
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public: |
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SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3); |
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|
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std::string getSelection1() const {return sele1_;} |
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std::string getSelection2() const {return sele2_;} |
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std::string getSelection3() const {return sele3_;} |
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RealType calcSCD(Snapshot* snapshot); |
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|
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private: |
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|
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std::string sele1_; |
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std::string sele2_; |
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std::string sele3_; |
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bool usePeriodicBoundaryConditions_; |
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|
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typedef tuple3<StuntDouble*, StuntDouble*, StuntDouble*> SDTuple3; |
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|
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std::vector<SDTuple3> tuples_; |
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}; |
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|
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|
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class SCDOrderParameter : public StaticAnalyser{ |
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public: |
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SCDOrderParameter(SimInfo* info, const std::string& filename, |
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const std::string& sele1, const std::string& sele2, const std::string& sele3); |
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|
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SCDOrderParameter(SimInfo* info, const std::string& filename, |
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const std::string& molname, int beginIndex, int endIndex); |
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virtual void process(); |
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|
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private: |
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void writeSCD(); |
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|
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std::vector<SCDElem> scdElems_; |
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std::vector<RealType> scdParam_; |
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|
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Snapshot* currentSnapshot_; |
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|
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|
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}; |
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} |
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|
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#endif |
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